Table 1. Yeast regulatory modules with regulators enriched with physical or genetic interactions.
| Module ID | #genes | TF | Signaling | ChIP | Annotation |
| 19 | 114 | KAR4, RSC3, SNF4, MET18, SWI6, SKO1, HAL9 | SHO1, GCN20, PRR1, YPK1, MCK1 | ABF1 | glycerolipid biosynthesis, protein transport and localization |
| 2 | 42 | SWI4, STE12, ASH1, SWI6, DIG1 | GAL83, PCL10, CDC42, CLN1, WSC2, RGS2, CLN2, CLB2, HOG1 | GZF3, GAL80 | protein glycolsylation, fungal cell wall organization |
| 83 | 45 | PDR3, UGA3, LYS14, MET32, GAT1, MET28, YAP5, IME1, DAL80, HIR2 | MET32, GCN4, GLN3, CBF1, ARG81, MET4, DAL82, TYE7, MET31 | sulfur and methionine metabolism, serine and aspartate amino acid metabolism | |
| 68 | 13 | ASH1 | STE2, SIC1 | SWI5, STE12, ACE2, MCM1, FKH2 | cell wall organization and bioenesis, cytokinesis |
| 100 | 7 | KAR4 | STE2 | STE12, DIG1 | response to pheromone, sexual reproduction |
| 30 | 64 | YHP1, GCN4, YFL052W, GSM1, HAP4, GAL80, WTM1, AFT2, ARR1 | REG2, PCL7, FAR1, GAC1 | HAP3, HAP2, SKN7, SIP4, HAP4, HAP1, MOT3, HAP5, AFT2, ROX1 | purine metabolism and mitochondrial ATP synthesis, respiration, purine nucleotide metabolic process |
| 31 | 22 | GIS1, GCN4, BAS1 | PPH3, YVH1 | ribosome biogenesis, RNA metabolism | |
| 34 | 14 | SWI5 | CDC20, CDC5 | SWI4, STE12, FKH1, SWI6, MCM1, FKH2, NDD1 | cell division, cell cycle, M phase |
| 36 | 96 | SNF4, IME4, SKO1 | RDI1, CKB1, CKA1, CNB1, ARP9, PLP25 | protein transport and localization | |
| 37 | 29 | UGA3, MSN1, TYE7, USV1 | HOG1, BMH1, PPT1, MCK1, CMK2 | GCR2, TYE7 | glycolysis, gluconeogenesis |
| 44 | 62 | OPI1, MET18 | GCN1,PPT1 | protein localization and transport, RNA transport | |
| 53 | 15 | RDS1, STB5, YAP1, YJL206C | SGD1 | YAP6, MSN4, YAP1, MSN2, YAP7 | alcohol dehydrogenase genes |
| 72 | 13 | SHP1, SLT2, CNB1 | REB1, RPN4 | proteolysis, ubiquitin dependent protein catabolism |
Each row corresponds to a Module. The first row specifies the Module ID, the second column has the module genes, the third column has the TF regulators predicted by MERLIN, the fourth column has the signaling proteins predicted by MERLIN, the fifth column has regulators predicted based on ChIP-chip, and the last column has a summary of the Gene Ontology terms associated with each module.